The number of variations in the pan-genome is reduced compared to the variations in the input VCF file

Question

[Wenke]

Do vg filter out some variants during the construction of the pan-genome, and if so, what are the criteria for filtering? The number of variations in the pan-genome is reduced compared to the variations in the input VCF file. The command I used is "vg autoindex --workflow giraffe -v sv.vcf -r ref.genome -p sv -t 64" The number of variants decreased by almost half after undergoing vg deconstruct compared to the number of variants in the VCF used to construct the pan-genome graph. What could be the reason for this?

Answer 1

[Jordan M Eizenga]

If variants overlap in the genome, vg deconstruct will combine them into one locus with multiple alleles. If your input VCF has a lot of deletions, that's probably what the cause is.